Sequencing of DNA requires large amounts of extracted DNA for use in the preparation of a sequencing library. The process of culturing cells, lysing the cells, extracting DNA, fragmenting the DNA, ligating linkers, and purification of the sequencing template is a multi-step process that can take several days to be performed by a skilled research technician. The challenge of sequence based detection is that existing whole genome sequencing systems such as the Roche 454 require several days of sample preparation and several days for sequencing. FIG. 1 shows a flow chart demonstrating the lengthy process now involved in sample preparation for next-generation sequencing techniques, such as the Roche 454 method. As shown in this figure, it can take one day for sample pretreatment; cell lysis; nucleic acid extraction; and whole genome amplification (WGA). It can then take one to five days for generating DNA libraries, which involves the following steps: DNA fragmentation; DNA end repair; adaptor ligation; fragment immobilization; nick repair; single-strand DNA isolation; and emulsion PCR titration. Finally, it can then take one to four days to prepare the sample for sequencing and the sequencing itself using the following steps: bulk emulsion PCR; break emulsion PCR; purify PCR positive beads; prepare beads for sequencing; and performing the sequencing reaction.
What is needed are methods for preparing DNA sequencing libraries that are faster and easier to perform and the integration of these methods with the sequencers.